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Sample GSM7661283 Query DataSets for GSM7661283
Status Public on Feb 27, 2024
Title Kidney, neonatal littermate control 1
Sample type SRA
Source name Kidney
Organism Mus musculus
Characteristics tissue: Kidney
cell line: Cdh16-cre
cell type: kidney tubular cells
genotype: Control
treatment: vehicle treatment
rip antibody: anti-HA antibody
Treatment protocol Samples were then centrifuged at 10,000g for 10 min to collect a post-mitochondrial supernatant. 25μl of washed anti-HA antibody-conjugated magnetic beads (Thermo ScientificTM; 88836) was added to the supernatant and incubated on an orbital shaker at 4°C overnight. The following day, samples were washed four times for 5 min in high salt buffer (50 mM Tris, pH 7.5, 300 mM KCl, 12 mM MgCl2, 1% Nonidet P-40, 1 mM DTT, 100 μg/mL cycloheximide) in a magnet on ice. After washing, the beads were resuspended in 500ul TRIzol® Reagent for total RNA isolation according the manufacturer’s instructions (Invitrogen).
Growth protocol Neonatal littermate control (Cdh16Cre;Foxp1fl/+;RiboTag) and Foxp1-deficient (Cdh16Cre;Foxp1fl/fl;RiboTag) animals were used for polysomes isolation analysis. Mice after hypothermic anaesthesia were perfused with PBS. The kidneys were quickly removed, homogenized in 400μl polysome buffer (50mM Tris, pH 7.5, 100mM KCl, 12mM MgCl2, 1% Nonidet P-40, 1mM DTT, 200U/ml RNasin (N2615; Promega), 1 mg/ml heparin, 100μg/ml cyclohexamide, and 1 x protease inhibitor (Roche; 04693132001)) using pellet pestles.
Extracted molecule total RNA
Extraction protocol The total RNA quality was determined by 2100 Bioanalyzer (Agilent) and quantified using the ND-2000 (NanoDrop Technologies).
RNA-seq transcriptome library was prepared following TruSeqTM RNA sample preparation Kit from Illumina (San Diego, CA) according to the manufacturer’s instructions.
Library strategy RIP-Seq
Library source transcriptomic
Library selection other
Instrument model Illumina NovaSeq 6000
Data processing Illumina HiSeq xten/NovaSeq 6000 sequencer
The raw paired-end reads were quality checked by FastQC ( and trimmed to remove adaptor sequences and low-quality reads using Trimmomatic with the default setting.
Then clean reads were mapped to the mouse reference genome GRCm38.86 using the STAR aligner. Only uniquely mapped reads were selected by SAMtools to minimize the rate of false positives.
Deeptools was used to generate a bigwig format to facilitate visualization of the reads coverage and comparison among different samples.
To identify differential expression genes (DEGs) between two different conditions, the raw read count file generated by featureCounts was used as an input for DESeq2, followed by standard differential expression analysis. Genes with Q value≤ 0.05 and |log2FC|>1 (DESeq2) were considered to be significantly different expressed genes.
Gene Ontology (GO) functional-enrichment analysis was performed using the R package clusterProfiler to identify which DEGs were significantly enriched in GO terms and metabolic pathways at Bonferroni-corrected P-value ≤0.05 compared with all the expressed genes as background.
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes the raw read count file generated by featureCounts
Supplementary files format and content: bigwig files to view the data
Submission date Jul 26, 2023
Last update date Feb 27, 2024
Contact name RENHUA SONG
Phone 61452667663
Organization name Centenary Institute
Lab Epigenetics and RNA Biology Program
Street address Charles Perkins Centre - D17, Level 4 West. The University of Sydney Johns Hopkins Drive
City Camperdown
State/province NSW
ZIP/Postal code 2050
Country Australia
Platform ID GPL24247
Series (2)
GSE238266 Identification of expression patterns of FoxP1 in the kidneys using RiboTag mice and RNA sequencing
GSE238268 Foxp1 is required for renal intercalated cell differentiation and acid-base regulation
BioSample SAMN36708624
SRA SRX21159265

Supplementary file Size Download File type/resource 13.1 Mb (ftp)(http) BW
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record
Processed data provided as supplementary file

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